Color volume series by per voxel variance?
Hi all,
Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame?
When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way.
Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume.
Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible?
Cheers Oli
Hi Oli, Not to my knowledge... The closest thing I can think of is ChimeraX "volume localCorrelation" (or in Chimera, "vop localCorrelation"), which compares two maps, and probably just opened as separate datasets rather than as part of a series: https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#localCorrelation
ChimeraX has a "vseries measure" command but it gives centroids, surface areas, and enclosed volumes for the individual maps rather than any collective measures of variability. https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html#measure
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 23, 2021, at 8:13 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi all,
Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame?
When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way.
Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume.
Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible?
Cheers Oli
Thanks Elaine - maybe that will work... calculating a local correlation value between the first and last frame and then coloring all frames by volume data value. Will give it a go!
Cheers Oli
On Nov 23, 2021, at 11:33 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Oli, Not to my knowledge... The closest thing I can think of is ChimeraX "volume localCorrelation" (or in Chimera, "vop localCorrelation"), which compares two maps, and probably just opened as separate datasets rather than as part of a series: https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#localCorrelation
ChimeraX has a "vseries measure" command but it gives centroids, surface areas, and enclosed volumes for the individual maps rather than any collective measures of variability. https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html#measure
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 23, 2021, at 8:13 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi all,
Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame?
When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way.
Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume.
Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible?
Cheers Oli
Hi Oli,
Here is something similar I tried to see the motion in lightsheet microscopy of neutrophil-like cells crawling in collagen.
https://www.cgl.ucsf.edu/chimera/data/mullins/cactus-oct2014/cactus.html https://www.cgl.ucsf.edu/chimera/data/mullins/cactus-oct2014/cactus.html
Done with the ChimeraX (or Chimera) measure motion command
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#motion https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#motion
Tom
On Nov 23, 2021, at 8:40 AM, Oliver Clarke via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Thanks Elaine - maybe that will work... calculating a local correlation value between the first and last frame and then coloring all frames by volume data value. Will give it a go!
Cheers Oli
On Nov 23, 2021, at 11:33 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Oli, Not to my knowledge... The closest thing I can think of is ChimeraX "volume localCorrelation" (or in Chimera, "vop localCorrelation"), which compares two maps, and probably just opened as separate datasets rather than as part of a series: https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#localCorrelation
ChimeraX has a "vseries measure" command but it gives centroids, surface areas, and enclosed volumes for the individual maps rather than any collective measures of variability. https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html#measure
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 23, 2021, at 8:13 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi all,
Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame?
When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way.
Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume.
Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible?
Cheers Oli
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
It would not be hard for ChimeraX to compute the per-pixel variance map with a little Python script. Then you could use that to color your movie map surface by variance map value.
Tom
On Nov 23, 2021, at 8:40 AM, Oliver Clarke via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Thanks Elaine - maybe that will work... calculating a local correlation value between the first and last frame and then coloring all frames by volume data value. Will give it a go!
Cheers Oli
On Nov 23, 2021, at 11:33 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Oli, Not to my knowledge... The closest thing I can think of is ChimeraX "volume localCorrelation" (or in Chimera, "vop localCorrelation"), which compares two maps, and probably just opened as separate datasets rather than as part of a series: https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#localCorrelation
ChimeraX has a "vseries measure" command but it gives centroids, surface areas, and enclosed volumes for the individual maps rather than any collective measures of variability. https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html#measure
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 23, 2021, at 8:13 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi all,
Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame?
When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way.
Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume.
Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible?
Cheers Oli
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Thanks Tom for the cactus idea I will give that a go! Not sure where to start with computing the per pixel variance but will do some digging into the docs
Cheers Oli
On Nov 23, 2021, at 1:06 PM, Tom Goddard goddard@sonic.net wrote:
It would not be hard for ChimeraX to compute the per-pixel variance map with a little Python script. Then you could use that to color your movie map surface by variance map value.
Tom
On Nov 23, 2021, at 8:40 AM, Oliver Clarke via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Thanks Elaine - maybe that will work... calculating a local correlation value between the first and last frame and then coloring all frames by volume data value. Will give it a go!
Cheers Oli
On Nov 23, 2021, at 11:33 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Oli, Not to my knowledge... The closest thing I can think of is ChimeraX "volume localCorrelation" (or in Chimera, "vop localCorrelation"), which compares two maps, and probably just opened as separate datasets rather than as part of a series: https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#localCorrelation
ChimeraX has a "vseries measure" command but it gives centroids, surface areas, and enclosed volumes for the individual maps rather than any collective measures of variability. https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html#measure
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 23, 2021, at 8:13 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi all,
Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame?
When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way.
Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume.
Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible?
Cheers Oli
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Here is an example Python script to add a "volume variance" command to ChimeraX.
https://rbvi.github.io/chimerax-recipes/variance/variance.html https://rbvi.github.io/chimerax-recipes/variance/variance.html
Tom
On Nov 23, 2021, at 3:08 PM, Oliver Clarke via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Thanks Tom for the cactus idea I will give that a go! Not sure where to start with computing the per pixel variance but will do some digging into the docs
Cheers Oli
On Nov 23, 2021, at 1:06 PM, Tom Goddard goddard@sonic.net wrote:
It would not be hard for ChimeraX to compute the per-pixel variance map with a little Python script. Then you could use that to color your movie map surface by variance map value.
Tom
On Nov 23, 2021, at 8:40 AM, Oliver Clarke via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Thanks Elaine - maybe that will work... calculating a local correlation value between the first and last frame and then coloring all frames by volume data value. Will give it a go!
Cheers Oli
On Nov 23, 2021, at 11:33 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Oli, Not to my knowledge... The closest thing I can think of is ChimeraX "volume localCorrelation" (or in Chimera, "vop localCorrelation"), which compares two maps, and probably just opened as separate datasets rather than as part of a series: https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#localCorrelation
ChimeraX has a "vseries measure" command but it gives centroids, surface areas, and enclosed volumes for the individual maps rather than any collective measures of variability. https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html#measure
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 23, 2021, at 8:13 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi all,
Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame?
When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way.
Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume.
Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible?
Cheers Oli
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Nice this exactly what I was looking for, thank you Tom!!
Cheers Oli
On Nov 24, 2021, at 3:27 AM, Tom Goddard goddard@sonic.net wrote:
Here is an example Python script to add a "volume variance" command to ChimeraX.
https://rbvi.github.io/chimerax-recipes/variance/variance.html
Tom
On Nov 23, 2021, at 3:08 PM, Oliver Clarke via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Thanks Tom for the cactus idea I will give that a go! Not sure where to start with computing the per pixel variance but will do some digging into the docs
Cheers Oli
On Nov 23, 2021, at 1:06 PM, Tom Goddard goddard@sonic.net wrote:
It would not be hard for ChimeraX to compute the per-pixel variance map with a little Python script. Then you could use that to color your movie map surface by variance map value.
Tom
On Nov 23, 2021, at 8:40 AM, Oliver Clarke via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Thanks Elaine - maybe that will work... calculating a local correlation value between the first and last frame and then coloring all frames by volume data value. Will give it a go!
Cheers Oli
On Nov 23, 2021, at 11:33 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Oli, Not to my knowledge... The closest thing I can think of is ChimeraX "volume localCorrelation" (or in Chimera, "vop localCorrelation"), which compares two maps, and probably just opened as separate datasets rather than as part of a series: https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#localCorrelation
ChimeraX has a "vseries measure" command but it gives centroids, surface areas, and enclosed volumes for the individual maps rather than any collective measures of variability. https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html#measure
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 23, 2021, at 8:13 AM, Oliver Clarke via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi all,
Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame?
When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way.
Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume.
Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible?
Cheers Oli
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Oliver Clarke -
Tom Goddard